Effect of the G.cntdot.T mismatch on backbone and sugar conformations of Z-DNA and B-DNA: analysis by Raman spectroscopy of crystal and solution structures of d(CGCGTG) and d(CGCGCG)

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Abstract
The Z-DNA crystal structures of d(CGCGTG) and d(CGCGCG) are compared by laser Raman spectroscopy. Raman bands originating from vibrations of the phosphodiester groups and sensitive to the DNA backbone conformation are similar for the two structures, indicating no significant perturbation to the Z-DNA backbone as a result of the incorporation of G.cntdot.T mismatches. Both Z structures also exhibit Raman markers at 625 and 670 cm-1, assigned respectively to C3''-endo/syn-dG (internal) and C2''-endo/syn-dG conformers (3'' terminus). Additional Raman intensity near 620 and 670 cm-1 in the spectrum of the d(CGCGTG) crystal is assigned to C4''-exo/syn-dG conformers at the mismatch sites (penultimate from the 5'' terminus). A Raman band at 1680 cm-1, detected only in the d(CGCGTG) crystal, is assigned to the hydrogen-bonded dT residues and is proposed as a definitive marker of the Z-DNA wobble G.cntdot.T pair. For aqueous solutions, the Raman spectra of d(CGCGTG) and d(CGCGCG) are those of B-DNA, but with significant differences between them. For example, the usual B-form marker band at 832 cm-1 in the spectrum of d(CGCGTG) is about 40% less intense than the corresponding band in the spectrum of d(CGCGCG), and the former structure exhibits a companion band at 864 cm-1 not observed for d-(CGCGCG). The simplest interpretation of these results is that the conventional B-form OPO geometry occurs for only 6 of the 10 OPO groups of d(CGCGTG). The remaining four OPO groups, believed to be those at or near the mismatch site, are in an "unusual B" conformation which generates the 864 cm-1 band. The B form of d(CGCGTG) also exhibits evidence of dG conformers differing from the usual C2''-endo/anti conformation. the data are consistent with C1''-exo/anti-dG conformers at the mismatch sites. The present findings indicate that the B helix (solution structure) is more significantly perturbed than the Z helix (crystal structure) by the incorporation of G.cntdot.T mismatches. The high resolution of the experimental data and its enhancement by the method of Fourier deconvolution confirm that a Raman band of very low intensity occurs near 806 .+-. 2 cm-1 in the B-DNA solution structures of both d(CTCGCG) and d(CGCGTG). This weak band contrasts sharply with the 12-fold more intense band near 807-810 cm-1 that is associated with the A-DNA backbone geometry (Benevides et al., 1986). Nonetheless, in quantitative analytical applications, the weak 806 cm-1 band should be taken into account in order to estimate accurately the percentages of B- and A-type backbone geometries, in accordance with the recent proposal of Nishimura et al. (1986).

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